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Games disappear from my GOG library and purchase history.

This has happened TWICE.

The first time it happened was with Stellaris and a bunch of DLC. The game just disappeared. I thought I maybe requested a refund, but I couldn't find anything. So I just brushed it off and bought it again.

Now, the second time was with Homeworld Collection. It doesn't even appear on my purchase history! This is insane! What the hell is going on with GOG? Is it a worm / virus ? Are you guys having database issues?!? This is insane.

I'm having to think TWICE before purchasing anything on GOG, because it might get deleted.

Sigh.
GoG sends you an email that confirms your every purchase on their site. Just make sure to contact the support team and show them your emails. as a proof of purchase.
Try using this

www.gog.com/user/refresh

many have said this clears up issues.
You did buy them from here, right? Not from a reseller? Just asking.
Once happen to me but the user refresh help me, yet the game was on my list... Now you still should have your mail ticket even if any problem happened, try to contact one of the blue.
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cleanpop: Stellaris and a bunch of DLC. [...] bought it again.
Ridiculous, especially considering the price tag involved.
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cleanpop: Are you guys having database issues?!?
If you didn't buy the games through a reseller, be sure to open a support ticket.

You can also open these links in a new tab, one at a time, while logged in a web browser:
https://www.gog.com/account/refresh
https://www.gog.com/user/refresh
There won't be a confirmation or anything after the pages load. Just check if the games are back in your library.

In addition to archiving your order confirmation e-mails, you should also get in the habit of printing your order receipts as PDF.
In the only time I had such an issue, I had to dig through all my back ups of gogrepo's databases, and then on my email history. After finding the missing game (and turns out a DLC too), I then contacted support about it, and they said there was an issue with that specific purchase (iirc, the problem was on their side), and offered me a refund and a custom discount code to get the contents by the price I had paid.

Luckily I had those gogrepo back ups and rarely delete my emails, but it could be a pretty big issue if I didn't have them any longer.